1zjw: Difference between revisions

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-[[Image:1zjw.gif|left|200px]]<br /><applet load="1zjw" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1zjw, resolution 2.500&Aring;" />
-'''Glutaminyl-tRNA synthetase complexed to glutamine and 2'deoxy A76 glutamine tRNA'''<br />
-==Overview==
+==Glutaminyl-tRNA synthetase complexed to glutamine and 2'deoxy A76 glutamine tRNA==
-Glutaminyl-tRNA synthetase generates Gln-tRNA(Gln) 10(7)-fold more efficiently than Glu-tRNA(Gln) and requires tRNA to synthesize the activated aminoacyl adenylate in the first step of the reaction. To examine the role of tRNA in amino acid activation more closely, several assays employing a tRNA analog in which the 2'-OH group at the 3'-terminal A76 nucleotide is replaced with hydrogen (tRNA(2'HGln)) were developed. These experiments revealed a 10(4)-fold reduction in kcat/Km in the presence of the analog, suggesting a direct catalytic role for tRNA in the activation reaction. The catalytic importance of the A76 2'-OH group in aminoacylation mirrors a similar role for this moiety that has recently been demonstrated during peptidyl transfer on the ribosome. Unexpectedly, tracking of Gln-AMP formation utilizing an alpha-32P-labeled ATP substrate in the presence of tRNA(2'HGln) showed that AMP accumulates 5-fold more rapidly than Gln-AMP. A cold-trapping experiment revealed that the nonenzymatic rate of Gln-AMP hydrolysis is too slow to account for the rapid AMP formation; hence, the hydrolysis of Gln-AMP to form glutamine and AMP must be directly catalyzed by the GlnRS x tRNA(2'HGln) complex. This hydrolysis of glutaminyl adenylate represents a novel reaction that is directly analogous to the pre-transfer editing hydrolysis of noncognate aminoacyl adenylates by editing synthetases such as isoleucyl-tRNA synthetase. Because glutaminyl-tRNA synthetase does not possess a spatially separate editing domain, these data demonstrate that a pre-transfer editing-like reaction can occur within the synthetic site of a class I tRNA synthetase.
+<StructureSection load='1zjw' size='340' side='right'caption='[[1zjw]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1zjw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZJW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZJW FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zjw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zjw OCA], [https://pdbe.org/1zjw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zjw RCSB], [https://www.ebi.ac.uk/pdbsum/1zjw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zjw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYQ_ECOLI SYQ_ECOLI]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zj/1zjw_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1zjw ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-ZJW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=AMP:'>AMP</scene> and <scene name='pdbligand=GLN:'>GLN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZJW OCA].
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-==Reference==
+__TOC__
-tRNA-dependent aminoacyl-adenylate hydrolysis by a nonediting class I aminoacyl-tRNA synthetase., Gruic-Sovulj I, Uter N, Bullock T, Perona JJ, J Biol Chem. 2005 Jun 24;280(25):23978-86. Epub 2005 Apr 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15845536 15845536]
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Glutamine--tRNA ligase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Bullock T]]
-[[Category: Bullock, T.]]
+[[Category: Gruic-Sovulj I]]
-[[Category: Gruic-Sovulj, I.]]
+[[Category: Perona JJ]]
-[[Category: Perona, J J.]]
+[[Category: Uter N]]
-[[Category: Uter, N.]]
-[[Category: AMP]]
-[[Category: GLN]]
-[[Category: SO4]]
-[[Category: protein-rna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:16:17 2008''